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Merge pull request #19 from AllenCell/py312_313_support
Py312 313 support
2 parents 309836c + ae8f553 commit 79355c8

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‎.github/workflows/build-docs.yml‎

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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/[email protected]
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with:
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persist-credentials: false
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- name: Set up Python
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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pip install --upgrade pip
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pip install .[dev]
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- name: Generate Docs
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run: |
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make gen-docs
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touch docs/_build/html/.nojekyll
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- name: Publish Docs
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uses: JamesIves/[email protected]
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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BASE_BRANCH: main # The branch the action should deploy from.
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BRANCH: gh-pages # The branch the action should deploy to.
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FOLDER: docs/_build/html/ # The folder the action should deploy.
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- name: Checkout Repository
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uses: actions/checkout@v3
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with:
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persist-credentials: false
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.12'
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cache: 'pip'
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[dev]
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- name: Generate Docs
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run: |
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make gen-docs
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touch docs/_build/html/.nojekyll
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- name: Publish Docs
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uses: JamesIves/[email protected]
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with:
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branch: gh-pages
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folder: docs/_build/html/
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token: ${{ secrets.GITHUB_TOKEN }}
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clean: true

‎.github/workflows/build-main.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Test with pytest
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run: |
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pytest --cov-report xml --cov=aicsshparam aicsshparam/tests/
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- name: Upload codecov
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uses: codecov/codecov-action@v1
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- uses: actions/checkout@v3
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# Set up Python using setup-python
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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# Install Python dependencies
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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# Run Pytest with coverage
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- name: Test with pytest
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run: |
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pytest --cov-report xml --cov=aicsshparam aicsshparam/tests/
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# Upload Code Coverage
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- name: Upload Code Coverage
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uses: codecov/codecov-action@v3
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lint:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with flake8
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run: |
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flake8 aicsshparam --count --verbose --show-source --statistics
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- name: Check with black
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run: |
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black --check aicsshparam
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with Flake8
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run: |
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flake8 aicsshparam --count --verbose --show-source --statistics
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- name: Check with Black
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run: |
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black --check aicsshparam
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publish:
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if: "contains(github.event.head_commit.message, 'Bump version')"
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if: contains(github.event.head_commit.message, 'Bump version')
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needs: [test, lint]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel
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- name: Build Package
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run: |
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python setup.py sdist bdist_wheel
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.12'
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools wheel
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- name: Build Package
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run: |
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python setup.py sdist bdist_wheel
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- name: Publish to PyPI
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}

‎.github/workflows/test-and-lint.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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python-version: ["3.9", "3.10", "3.11"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Test with pytest
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run: |
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pytest aicsshparam/tests/
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- name: Upload codecov
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uses: codecov/codecov-action@v1
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- name: Checkout Repository
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uses: actions/checkout@v3
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# Set up Python using setup-python
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Test with pytest
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run: |
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pytest aicsshparam/tests/
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- name: Upload Code Coverage
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uses: codecov/codecov-action@v3
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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lint:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
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with:
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python-version: 3.9
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with flake8
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run: |
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flake8 aicsshparam --count --verbose --show-source --statistics
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- name: Check with black
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run: |
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black --check aicsshparam
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- name: Checkout Repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .[test]
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- name: Lint with Flake8
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run: |
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flake8 aicsshparam --count --verbose --show-source --statistics
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- name: Check with Black
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run: |
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black --check aicsshparam

‎CONTRIBUTING.md‎

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## Deploying
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A reminder for the maintainers on how to deploy.
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Make sure all your changes are committed.
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Then run:
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1. **Ensure all changes are committed.**
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Refer to [bump2version on PyPI](https://pypi.org/project/bump2version/) for more details on versioning.
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2. **Bump the version number.**
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Run one of the following commands depending on the type of version update:
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```bash
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bump2version major # for major releases with breaking changes
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bump2version minor # for minor releases with new features
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bump2version patch # for patch releases with bug fixes
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```
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3. **Push the changes and tags to the repository.**
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```bash
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git push
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git push --tags
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```
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---
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**Note:**
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Sometimes, you might encounter situations where there are uncommitted changes or modifications in your working directory that you intend to include in the release. In such cases, you can use the `--allow-dirty` flag with `bump2version` to permit version bumping even when the working directory isn't clean:
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```bash
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bump2version patch # possible: major / minor / patch
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git push
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git push --tags
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bump2version patch --allow-dirty
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```
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This will release a new package version on Git + GitHub and publish to PyPI.

‎README.md‎

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## Installation:
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## Build Dependencies for Python 3.13.*
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If you are using Python 3.13.*, you will need to install the following build dependencies:
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- **fftw**
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- **openblas**
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- **cmake**
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- **pkg-config**
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One convenient way to install these dependencies is by using Conda. You can run the following command:
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```bash
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conda install -c conda-forge fftw openblas cmake pkg-config
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```
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**Stable Release**: `pip install aicsshparam`
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**Build from source to make customization**:

‎aicsshparam/__init__.py‎

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__email__ = "[email protected]"
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# Do not edit this string manually, always use bumpversion
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# Details in CONTRIBUTING.md
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__version__ = "0.1.10"
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__version__ = "0.1.11"
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def get_module_version():

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